Publications

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2022 August
A nanopore interface for higher bandwidth DNA computing
  • Karen Zhang
  • Yuan-Jyue Chen
  • Delaney Wilde
  • Kathryn Doroschak
  • Karin Strauss
  • Luis Ceze
  • Georg Seelig
  • Jeff Nivala
Nature Communications.
2022 July
Recording gene expression order in DNA by CRISPR addition of retron barcodes
  • Santa Bhattarai-Kline
  • Sierra K. Lear
  • Chloe B. Fishman
  • Santiago C. Lopez
  • Elana R. Lockshin
  • Max G. Schubert
  • Jeff Nivala
  • George M. Church
  • Seth L. & Shipman
Nature.
2022 May
Passively sensing SARS-CoV-2 RNA in public transit buses
  • Jason S Hoffman
  • Matthew Hirano
  • Nuttada Panpradist
  • Joseph Breda
  • Parker Ruth
  • Yuanyi Xu
  • Jonathan Lester
  • Bichlien H Nguyen
  • Luis Ceze
  • Shwetak N Patel
Science of the Total Environment.
2022 April
Doctoring Direct-to-Consumer Genetic Tests with DNA Spike-Ins
  • Peter Ney
  • Arkaprabha Bhattacharya
  • David Ward
  • Luis Ceze
  • Tadayoshi Kohno
  • Jeff Nivala
biorxiv.
Preprint
2022 January
Synthetic DNA applications in information technology
  • Linda C. Meiser
  • Bichlien H. Nguyen
  • Yuan-Jyue Chen
  • Jeff Nivala
  • Karin Strauss
  • Luis Ceze
  • Robert N. Grass
Nature Communications.
Review
2021 November
Scaling DNA data storage with nanoscale electrode wells
  • Bichlien H. Nguyen
  • Christopher N. Takahashi
  • Gagan Gupta
  • Jake A. Smith
  • Richard Rouse
  • Paul Berndt
  • Sergey Yekhanin
  • David P. Ward
  • Siena D. Ang
  • Patrick Garvan
  • Hsing-Yeh Parker
  • Rob Carlson
  • Douglas Carmean
  • Luis Ceze
  • Karin Strauss
Science Advances.
2021 August
Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis
  • Keisuke Motone
  • Nicolas Cardozo
  • Jeff Nivala
iScience.
Review
2021 August
Multiplexed direct detection of barcoded protein reporters on a nanopore array
  • Nick Cardozo
  • Karen Zhang
  • Katie Doroschak
  • Aerilynn Nguyen
  • Zoheb Siddiqui
  • Nicholas Bogard
  • Karin Strauss
  • Luis Ceze
  • Jeff Nivala
Nature Biotechnology.
2021 May
DNA Sequencing Flow Cells and the Security of the Molecular-Digital Interface
  • Peter Ney
  • Lee Organick
  • Jeff Nivala
  • Luis Ceze
  • Tadayoshi Kohno
Privacy Enhancing Technologies Symposium.
2021 February
Absolute and arbitrary orientation of single-molecule shapes
  • Ashwin Gopinath
  • Chris Thachuk
  • Anya Mitskovets
  • Harry A. Atwater
  • David Kirkpatrick
  • Paul W. K. Rothemund
Science.
2021 January
An empirical comparison of preservation methods for synthetic DNA data storage
  • Lee Organick
  • Bichlien Nguyen
  • Rachel McAmis
  • Weida Chen
  • A. Xavier Kohll
  • Siena Dumas Ang
  • Robert Grass
  • Luis Ceze
  • Karin Strauss
Small Methods.
2020 November
Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures
  • Kathryn Doroschak
  • Karen Zhang
  • Melissa Queen
  • Aishwarya Mandyam
  • Karin Strauss
  • Luis Ceze
  • Jeff Nivala
Nature Communications.
2020 June
PurpleDrop: A Digital Microfluidics-Based Platform for Hybrid Molecular-Electronics Applications
  • Ashley Stephenson
  • Max Willsey
  • Jeff McBride
  • Sharon Newman
  • Bichlien Nguyen
  • Christopher Takahashi
  • Karin Strauss
  • Luis Ceze
IEEE Micro.
2020 June
Quantifying molecular bias in DNA data storage
  • Yuan-Jyue Chen
  • Christopher Takahashi
  • Lee Organick
  • Callista Bee
  • Siena Dumas Ang
  • Patrick Weiss
  • Bill Peck
  • Georg Seelig
  • Luis Ceze
  • Karin Strauss
Nature Communications.
2020 June
Follow the barcoded microbes
  • Jeff Nivala
Science.
2020 May
Content-Based Similarity Search in Large-Scale DNA Data Storage Systems
  • Callista Bee
  • Yuan-Jyue Chen
  • David Ward
  • Xiaomeng Liu
  • Georg Seelig
  • Karin Strauss
  • Luis Ceze
bioRxiv.
Preprint.
2020 March
Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands
  • Kathryn Doroschak
  • Karen Zhang
  • Melissa Queen
  • Aishwarya Mandyam
  • Karin Strauss
  • Luis Ceze
  • Jeff Nivala
bioRxiv.
Preprint.
2020 January
Probing the physical limits of reliable DNA data retrieval
  • Lee Organick
  • Yuan-Jyue Chen
  • Siena Dumas Ang
  • Randolph Lopez
  • Xiaomeng Liu
  • Karin Strauss
  • Luis Ceze
Nature Communications.
2019 November
Multiplexed direct detection of barcoded protein reporters on a nanopore array
  • Nick Cardozo
  • Karen Zhang
  • Katie Doroschak
  • Aerilynn Nguyen
  • Zoheb Siddiqui
  • Karin Strauss
  • Luis Ceze
  • Jeff Nivala
bioRxiv.
Preprint.
2019 November
Scaling Microfluidics to Complex, Dynamic Protocols
  • Max Willsey
  • Ashley Stephenson
  • Chris Takahashi
  • Bichlien Nguyen
  • Karin Strauss
  • Luis Ceze
2019 IEEE/ACM International Conference on Computer-Aided Design (ICCAD).
Invited Paper
2019 September
Demonstration of End-to-End Automation of DNA Data Storage
  • Christopher N Takahashi
  • Bichlien H Nguyen
  • Karin Strauss
  • Luis H Ceze
Scientific Reports.
2019 July
DNA assembly for nanopore data storage readout
  • Randolph Lopez
  • Yuan-Jyue Chen
  • Siena Dumas Ang
  • Sergey Yekhanin
  • Konstantin Makarychev
  • Miklos Z Racz
  • Georg Seelig
  • Karin Strauss
  • Luis Ceze
Nature Communications.
2019 May
Molecular digital data storage using DNA
  • Luis Ceze
  • Jeff Nivala
  • Karin Strauss
Nature Reviews Genetics.
2019 April
High density DNA data storage library via dehydration with digital microfluidic retrieval
  • Sharon Newman
  • Ashley P Stephenson
  • Max Willsey
  • Bichlien H Nguyen
  • Christopher N Takahashi
  • Karin Strauss
  • Luis Ceze
Nature Communications.
2019 April
Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidics Platform
  • Max Willsey
  • Ashley P. Stephenson
  • Christopher N. Takahashi
  • Pranav Vaid
  • Bichlien H. Nguyen
  • Michal Piszczek
  • Christine Betts
  • Sharon Newman
  • Sarang Joshi
  • Karin Strauss
  • Luis Ceze
Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems . ASPLOS '19
2019 January
DNA Data Storage and Hybrid Molecular-Electronic Computing
  • Douglas Carmean
  • Luis Ceze
  • Georg Seelig
  • Callista Bee
  • Karin Strauss
  • Max Willsey
Proceedings of the IEEE.
2018 October
A Content-Addressable DNA Database With Learned Sequence Encodings
  • Callista Bee
  • Yuan-Jyue Chen
  • David Ward
  • Xiaomeng Liu
  • Georg Seelig
  • Karin Strauss
  • Luis Ceze
24th International Conference On DNA Computing and Molecular Programming (DNA24).
2018 February
Random access in large-scale DNA data storage
  • Lee Organick
  • Siena Dumas Ang
  • Yuan-Jyue Chen
  • Randolph Lopez
  • Sergey Yekhanin
  • Konstantin Makarychev
  • Miklos Z. Racz
  • Govinda Kamath
  • Parikshit Gopalan
  • Bichlien Nguyen
  • Christopher Takahashi
  • Sharon Newman
  • Hsing-Yeh Parker
  • Cyrus Rashtchian
  • Callista Bee
  • Gagan Gupta
  • Robert Carlson
  • John Mulligan
  • Douglas Carmean
  • Georg Seelig
  • Luis Ceze
  • Karin Strauss
Nature Biotechnology.
2017 November
Clustering Billions of Reads for DNA Data Storage
  • Cyrus Rashtchian
  • Konstantin Makarychev
  • Miklos Racz
  • Siena Ang
  • Djordje Jevdjic
  • Sergey Yekhanin
  • Luis Ceze
  • Karin Strauss
NIPS.
2017 August
Computer Security, Privacy, and DNA Sequencing: Compromising Computers with Synthesized DNA, Privacy Leaks, and More
  • Peter Ney
  • Karl Koscher
  • Lee Organick
  • Luis Ceze
  • Tadayoshi Kohno
USENIX Security.
2017 March
Scaling up DNA data storage and random access retrieval
  • Lee Organick
  • Siena Dumas Ang
  • Yuan-Jyue Chen
  • Randolph Lopez
  • Sergey Yekhanin
  • Konstantin Makarychev
  • Miklos Z. Racz
  • Govinda Kamath
  • Parikshit Gopalan
  • Bichlien Nguyen
  • Christopher Takahashi
  • Sharon Newman
  • Hsing-Yeh Parker
  • Cyrus Rashtchian
  • Callista Bee
  • Gagan Gupta
  • Robert Carlson
  • John Mulligan
  • Douglas Carmean
  • Georg Seelig
  • Luis Ceze
  • Karin Strauss
bioRxiv.
Accepted for publication at Nature Biotechnology.
2016 April
A DNA-Based Archival Storage System
  • James Bornholt
  • Randolph Lopez
  • Karin Strauss
  • Douglas M Carmean
  • Luis Ceze
  • Georg Seelig
  • Karin Strauss
International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS).
Selected for IEEE Micro Top Picks 2016.

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